Slightly longer answer: the Manuscripts file container isn't just a text document but contains a bunch of metadata and versioning information; you can look at the files inside with right click -> show package contents.

@Adam-Buckley, @Amafortas: the document also contains a full version history. You can trim the version history by going to File > Reduce File Size. There is no harm in doing that really – Manuscripts documents are also compatible with the macOS provided document versioning so you can still revert to older versions of the document. The full version history is kept for future features mainly, most importantly for the ability to merge diverged versions of the document amongst collaborators in a future update.